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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TCGAutils_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TCGAutils.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAutils/DESCRIPTION' ... OK
* this is package 'TCGAutils' version '1.10.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TCGAutils' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'GenomicRanges:::.normarg_field'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       46.36   2.66   50.37
trimColData                        34.66   6.18   42.16
TCGAprimaryTumors                  31.77   2.75   37.01
curatedTCGAData-helpers            24.99   0.87   27.06
imputeAssay                        23.61   0.83   25.48
oncoPrintTCGA                      20.56   0.89   23.43
makeSummarizedExperimentFromGISTIC  5.07   0.52   20.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       50.08   3.05   54.45
TCGAprimaryTumors                  34.35   1.78   37.65
trimColData                        31.47   0.94   33.91
imputeAssay                        29.41   0.74   31.22
curatedTCGAData-helpers            24.34   0.75   26.33
oncoPrintTCGA                      21.03   0.79   23.88
makeSummarizedExperimentFromGISTIC  6.46   0.31   21.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/TCGAutils.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/TCGAutils_1.10.1.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.10.1.zip && rm TCGAutils_1.10.1.tar.gz TCGAutils_1.10.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 66342  100 66342    0     0  1290k      0 --:--:-- --:--:-- --:--:-- 1322k

install for i386

* installing *source* package 'TCGAutils' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAutils'
    finding HTML links ... done
    ID-translation                          html  
    TCGAbarcode                             html  
    TCGAbiospec                             html  
    TCGAprimaryTumors                       html  
    finding level-2 HTML links ... done

    TCGAsampleSelect                        html  
    TCGAutils-package                       html  
    builds                                  html  
    clinicalNames                           html  
    curatedTCGAData-helpers                 html  
    diseaseCodes                            html  
    findGRangesCols                         html  
    generateMap                             html  
    getFileName                             html  
    hidden-helpers                          html  
    imputeAssay                             html  
    makeGRangesListFromCopyNumber           html  
    makeGRangesListFromExonFiles            html  
    makeSummarizedExperimentFromGISTIC      html  
    mergeColData                            html  
    oncoPrintTCGA                           html  
    sampleTypes                             html  
    simplifyTCGA                            html  
    trimColData                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'TCGAutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAutils' as TCGAutils_1.10.1.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked